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GA4GH Genomics API

The GA4GH API attempts to gather together protocols and data models useful for genomics data interchange. It offers protocols that can be implemented over existing Genomics data stores to make these results more easily discovered, shared, and replicated.

Contents

• Introduction
  • Why use this web API?
  • If you need background
  • The GA4GH web API
  • Schemas and formats
• API Overview
  • API Design
  • API Goals
  • Reads
  • Variants
  • References
  • Sequence Annotations
  • Metadata
  • Allele Annotations
  • RNA Quantification
  • Genotype to Phenotype
• Installing the GA4GH Schemas
  • Generating Source Code
  • Installing the Documentation Tools and Generating Documentation
  • Generate the documentation
• Schemas
  • common
  • bio_metadata
  • bio_metadata_service
  • metadata
  • metadata_service
  • reads
  • read_service
  • references
  • reference_service
  • variants
  • variant_service
  • rna_quantification
  • rna_quantification_service
  • allele_annotations
  • allele_annotation_service
  • sequence_annotations
  • sequence_annotation_service
  • struct
  • genotype_phenotype
  • genotype_phenotype_service
• Appendix
  • Glossary
  • Use of Ontologies in GA4GH API
  • The JSON Format
  • Google Protocol Buffers
  • Code samples (stub)
  • Generating API Definitions